R Notebook

library(Seurat)

mat <- list()
mat$HC1 <- Read10X_h5(filename = "../data/COVID-19/GSM4475048_C51_filtered_feature_bc_matrix.h5")
mat$HC2 <- Read10X_h5(filename = "../data/COVID-19/GSM4475049_C52_filtered_feature_bc_matrix.h5")
mat$HC3 <- Read10X_h5(filename = "../data/COVID-19/GSM4475050_C100_filtered_feature_bc_matrix.h5")
mat$HC4 <- Read10X(data.dir = "../data/COVID-19/GSM3660650/")

mat$M1 <- Read10X_h5(filename = "../data/COVID-19/GSM4339769_C141_filtered_feature_bc_matrix.h5")
mat$M2 <- Read10X_h5(filename = "../data/COVID-19/GSM4339770_C142_filtered_feature_bc_matrix.h5")
mat$M3 <- Read10X_h5(filename = "../data/COVID-19/GSM4339772_C144_filtered_feature_bc_matrix.h5")

mat$S1 <- Read10X_h5(filename = "../data/COVID-19/GSM4339773_C145_filtered_feature_bc_matrix.h5")
mat$S2 <- Read10X_h5(filename = "../data/COVID-19/GSM4339771_C143_filtered_feature_bc_matrix.h5")
mat$S3 <- Read10X_h5(filename = "../data/COVID-19/GSM4339774_C146_filtered_feature_bc_matrix.h5")
mat$S4 <- Read10X_h5(filename = "../data/COVID-19/GSM4475051_C148_filtered_feature_bc_matrix.h5")
mat$S5 <- Read10X_h5(filename = "../data/COVID-19/GSM4475052_C149_filtered_feature_bc_matrix.h5")
mat$S6 <- Read10X_h5(filename = "../data/COVID-19/GSM4475053_C152_filtered_feature_bc_matrix.h5")

meta.data <- read.delim("../data/COVID-19/all.cell.annotation.meta.txt")
rownames(meta.data) <- meta.data$ID
head(meta.data)

numbering = c(HC1 = 1,
              HC2 = 2,
              HC3 = 3,
              HC4 = 4,
              M1 = 5,
              M2 = 6,
              M3 = 7,
              S1 = 9,
              S2 = 8,
              S3 = 10,
              S4 = 11,
              S5 = 12,
              S6 = 13)

for (i in names(mat)){
  colnames(mat[[i]]) <- gsub('-', '_', colnames(mat[[i]]))
  colnames(mat[[i]]) <- gsub('1', numbering[i], colnames(mat[[i]]))
}

for (i in names(mat)){
 mat[[i]] <- mat[[i]][, meta.data$ID[meta.data$sample_new == i]]
}

objs <- list()
for (i in names(mat)){
 objs[[i]] <- CreateSeuratObject(mat[[i]], project = i, meta.data = meta.data[meta.data$sample_new == i, ])
}

for (i in names(objs)) {
  objs[[i]] <- NormalizeData(objs[[i]], verbose=FALSE)
  objs[[i]] <- FindVariableFeatures(objs[[i]], selection.method = "vst", nfeatures = 2000, verbose=FALSE)

  objs[[i]] <- ScaleData(objs[[i]], verbose=FALSE)
  objs[[i]] <- RunPCA(objs[[i]], features = VariableFeatures(object = objs[[i]]), verbose=FALSE)
}

ptm = proc.time()
anchors <- FindIntegrationAnchors(object.list = objs, dims = 1:30)

Computing 2000 integration features
Scaling features for provided objects

  |                                                  | 0 % ~calculating  
  |++++                                              | 8 % ~11s          
  |++++++++                                          | 15% ~09s          
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  |++++++++++++++++++++                              | 38% ~04s          
  |++++++++++++++++++++++++                          | 46% ~03s          
  |+++++++++++++++++++++++++++                       | 54% ~02s          
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  |+++++++++++++++++++++++++++++++++++++++++++       | 85% ~01s          
  |+++++++++++++++++++++++++++++++++++++++++++++++   | 92% ~00s          
  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=06s  

Finding all pairwise anchors

  |                                                  | 0 % ~calculating  

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 22833 anchors
Filtering anchors
    Retained 4260 anchors
Extracting within-dataset neighbors

  |+                                                 | 1 % ~03h 26m 22s  

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 9322 anchors
Filtering anchors
    Retained 3843 anchors
Extracting within-dataset neighbors

  |++                                                | 3 % ~02h 14m 26s  

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 9570 anchors
Filtering anchors
    Retained 3148 anchors
Extracting within-dataset neighbors

  |++                                                | 4 % ~01h 48m 33s  

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 8829 anchors
Filtering anchors
    Retained 2084 anchors
Extracting within-dataset neighbors

  |+++                                               | 5 % ~01h 37m 40s  

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 9093 anchors
Filtering anchors
    Retained 1633 anchors
Extracting within-dataset neighbors

  |++++                                              | 6 % ~01h 30m 22s  

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 6187 anchors
Filtering anchors
    Retained 2540 anchors
Extracting within-dataset neighbors

  |++++                                              | 8 % ~01h 17m 33s  

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 10101 anchors
Filtering anchors
    Retained 2688 anchors
Extracting within-dataset neighbors

  |+++++                                             | 9 % ~01h 17m 53s  

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 11136 anchors
Filtering anchors
    Retained 2485 anchors
Extracting within-dataset neighbors

  |++++++                                            | 10% ~01h 17m 19s  

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 7221 anchors
Filtering anchors
    Retained 2977 anchors
Extracting within-dataset neighbors

  |++++++                                            | 12% ~01h 10m 30s  

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 5225 anchors
Filtering anchors
    Retained 2148 anchors
Extracting within-dataset neighbors

  |+++++++                                           | 13% ~01h 05m 20s  

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 10004 anchors
Filtering anchors
    Retained 2725 anchors
Extracting within-dataset neighbors

  |++++++++                                          | 14% ~01h 05m 30s  

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 11019 anchors
Filtering anchors
    Retained 2878 anchors
Extracting within-dataset neighbors

  |++++++++                                          | 15% ~01h 05m 16s  

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 7098 anchors
Filtering anchors
    Retained 3215 anchors
Extracting within-dataset neighbors

  |+++++++++                                         | 17% ~01h 01m 05s  

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 5410 anchors
Filtering anchors
    Retained 2697 anchors
Extracting within-dataset neighbors

  |+++++++++                                         | 18% ~57m 42s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 8838 anchors
Filtering anchors
    Retained 6318 anchors
Extracting within-dataset neighbors

  |++++++++++                                        | 19% ~55m 10s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 1686 anchors
Filtering anchors
    Retained 1169 anchors
Extracting within-dataset neighbors

  |+++++++++++                                       | 21% ~51m 50s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 1625 anchors
Filtering anchors
    Retained 1152 anchors
Extracting within-dataset neighbors

  |+++++++++++                                       | 22% ~48m 46s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 1551 anchors
Filtering anchors
    Retained 1409 anchors
Extracting within-dataset neighbors

  |++++++++++++                                      | 23% ~45m 31s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 1659 anchors
Filtering anchors
    Retained 1582 anchors
Extracting within-dataset neighbors

  |+++++++++++++                                     | 24% ~42m 36s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 1584 anchors
Filtering anchors
    Retained 1561 anchors
Extracting within-dataset neighbors

  |+++++++++++++                                     | 26% ~40m 02s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 1583 anchors
Filtering anchors
    Retained 1570 anchors
Extracting within-dataset neighbors

  |++++++++++++++                                    | 27% ~37m 41s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 26367 anchors
Filtering anchors
    Retained 1241 anchors
Extracting within-dataset neighbors

  |+++++++++++++++                                   | 28% ~45m 35s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 26799 anchors
Filtering anchors
    Retained 1217 anchors
Extracting within-dataset neighbors

  |+++++++++++++++                                   | 29% ~51m 59s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 10209 anchors
Filtering anchors
    Retained 1230 anchors
Extracting within-dataset neighbors

  |++++++++++++++++                                  | 31% ~51m 46s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 7223 anchors
Filtering anchors
    Retained 1563 anchors
Extracting within-dataset neighbors

  |+++++++++++++++++                                 | 32% ~51m 55s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 11207 anchors
Filtering anchors
    Retained 2663 anchors
Extracting within-dataset neighbors

  |+++++++++++++++++                                 | 33% ~52m 39s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 10738 anchors
Filtering anchors
    Retained 2434 anchors
Extracting within-dataset neighbors

  |++++++++++++++++++                                | 35% ~53m 10s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 1573 anchors
Filtering anchors
    Retained 662 anchors
Extracting within-dataset neighbors

  |++++++++++++++++++                                | 36% ~50m 55s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 26299 anchors
Filtering anchors
    Retained 649 anchors
Extracting within-dataset neighbors

  |+++++++++++++++++++                               | 37% ~57m 52s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 27070 anchors
Filtering anchors
    Retained 434 anchors
Extracting within-dataset neighbors

  |++++++++++++++++++++                              | 38% ~01h 03m 22s  

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 10568 anchors
Filtering anchors
    Retained 843 anchors
Extracting within-dataset neighbors

  |++++++++++++++++++++                              | 40% ~01h 02m 56s  

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 8402 anchors
Filtering anchors
    Retained 1157 anchors
Extracting within-dataset neighbors

  |+++++++++++++++++++++                             | 41% ~01h 02m 44s  

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 12195 anchors
Filtering anchors
    Retained 2172 anchors
Extracting within-dataset neighbors

  |++++++++++++++++++++++                            | 42% ~01h 03m 08s  

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 11602 anchors
Filtering anchors
    Retained 2178 anchors
Extracting within-dataset neighbors

  |++++++++++++++++++++++                            | 44% ~01h 03m 19s  

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 1662 anchors
Filtering anchors
    Retained 588 anchors
Extracting within-dataset neighbors

  |+++++++++++++++++++++++                           | 45% ~01h 00m 51s  

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 33458 anchors
Filtering anchors
    Retained 8485 anchors
Extracting within-dataset neighbors

  |++++++++++++++++++++++++                          | 46% ~01h 07m 37s  

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 5079 anchors
Filtering anchors
    Retained 1388 anchors
Extracting within-dataset neighbors

  |++++++++++++++++++++++++                          | 47% ~01h 04m 49s  

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 4935 anchors
Filtering anchors
    Retained 1223 anchors
Extracting within-dataset neighbors

  |+++++++++++++++++++++++++                         | 49% ~01h 02m 05s  

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 4470 anchors
Filtering anchors
    Retained 1642 anchors
Extracting within-dataset neighbors

  |+++++++++++++++++++++++++                         | 50% ~59m 08s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 4132 anchors
Filtering anchors
    Retained 2217 anchors
Extracting within-dataset neighbors

  |++++++++++++++++++++++++++                        | 51% ~56m 20s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 4306 anchors
Filtering anchors
    Retained 2336 anchors
Extracting within-dataset neighbors

  |+++++++++++++++++++++++++++                       | 53% ~53m 43s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 4217 anchors
Filtering anchors
    Retained 2202 anchors
Extracting within-dataset neighbors

  |+++++++++++++++++++++++++++                       | 54% ~51m 12s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 1367 anchors
Filtering anchors
    Retained 1001 anchors
Extracting within-dataset neighbors

  |++++++++++++++++++++++++++++                      | 55% ~48m 39s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 4981 anchors
Filtering anchors
    Retained 2589 anchors
Extracting within-dataset neighbors

  |+++++++++++++++++++++++++++++                     | 56% ~46m 49s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 5023 anchors
Filtering anchors
    Retained 3724 anchors
Extracting within-dataset neighbors

  |+++++++++++++++++++++++++++++                     | 58% ~45m 20s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 6316 anchors
Filtering anchors
    Retained 1430 anchors
Extracting within-dataset neighbors

  |++++++++++++++++++++++++++++++                    | 59% ~43m 27s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 6133 anchors
Filtering anchors
    Retained 1328 anchors
Extracting within-dataset neighbors

  |+++++++++++++++++++++++++++++++                   | 60% ~41m 37s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 5146 anchors
Filtering anchors
    Retained 2252 anchors
Extracting within-dataset neighbors

  |+++++++++++++++++++++++++++++++                   | 62% ~39m 33s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 4316 anchors
Filtering anchors
    Retained 2620 anchors
Extracting within-dataset neighbors

  |++++++++++++++++++++++++++++++++                  | 63% ~37m 35s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 5164 anchors
Filtering anchors
    Retained 2713 anchors
Extracting within-dataset neighbors

  |+++++++++++++++++++++++++++++++++                 | 64% ~35m 43s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 4944 anchors
Filtering anchors
    Retained 2755 anchors
Extracting within-dataset neighbors

  |+++++++++++++++++++++++++++++++++                 | 65% ~33m 55s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 1425 anchors
Filtering anchors
    Retained 1123 anchors
Extracting within-dataset neighbors

  |++++++++++++++++++++++++++++++++++                | 67% ~32m 03s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 6440 anchors
Filtering anchors
    Retained 4512 anchors
Extracting within-dataset neighbors

  |++++++++++++++++++++++++++++++++++                | 68% ~30m 42s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 6572 anchors
Filtering anchors
    Retained 5273 anchors
Extracting within-dataset neighbors

  |+++++++++++++++++++++++++++++++++++               | 69% ~29m 35s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 3769 anchors
Filtering anchors
    Retained 2991 anchors
Extracting within-dataset neighbors

  |++++++++++++++++++++++++++++++++++++              | 71% ~27m 53s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 7243 anchors
Filtering anchors
    Retained 1864 anchors
Extracting within-dataset neighbors

  |++++++++++++++++++++++++++++++++++++              | 72% ~26m 30s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 7933 anchors
Filtering anchors
    Retained 1712 anchors
Extracting within-dataset neighbors

  |+++++++++++++++++++++++++++++++++++++             | 73% ~25m 07s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 5622 anchors
Filtering anchors
    Retained 2619 anchors
Extracting within-dataset neighbors

  |++++++++++++++++++++++++++++++++++++++            | 74% ~23m 35s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 4755 anchors
Filtering anchors
    Retained 2521 anchors
Extracting within-dataset neighbors

  |++++++++++++++++++++++++++++++++++++++            | 76% ~22m 06s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 6506 anchors
Filtering anchors
    Retained 3267 anchors
Extracting within-dataset neighbors

  |+++++++++++++++++++++++++++++++++++++++           | 77% ~20m 41s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 6509 anchors
Filtering anchors
    Retained 3762 anchors
Extracting within-dataset neighbors

  |++++++++++++++++++++++++++++++++++++++++          | 78% ~19m 19s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 1588 anchors
Filtering anchors
    Retained 999 anchors
Extracting within-dataset neighbors

  |++++++++++++++++++++++++++++++++++++++++          | 79% ~17m 54s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 7063 anchors
Filtering anchors
    Retained 4446 anchors
Extracting within-dataset neighbors

  |+++++++++++++++++++++++++++++++++++++++++         | 81% ~16m 47s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 7510 anchors
Filtering anchors
    Retained 5062 anchors
Extracting within-dataset neighbors

  |++++++++++++++++++++++++++++++++++++++++++        | 82% ~15m 47s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 3786 anchors
Filtering anchors
    Retained 2505 anchors
Extracting within-dataset neighbors

  |++++++++++++++++++++++++++++++++++++++++++        | 83% ~14m 28s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 4647 anchors
Filtering anchors
    Retained 3203 anchors
Extracting within-dataset neighbors

  |+++++++++++++++++++++++++++++++++++++++++++       | 85% ~13m 11s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 8904 anchors
Filtering anchors
    Retained 1573 anchors
Extracting within-dataset neighbors

  |+++++++++++++++++++++++++++++++++++++++++++       | 86% ~12m 04s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 9349 anchors
Filtering anchors
    Retained 1460 anchors
Extracting within-dataset neighbors

  |++++++++++++++++++++++++++++++++++++++++++++      | 87% ~10m 57s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 6420 anchors
Filtering anchors
    Retained 2007 anchors
Extracting within-dataset neighbors

  |+++++++++++++++++++++++++++++++++++++++++++++     | 88% ~09m 45s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 5370 anchors
Filtering anchors
    Retained 2346 anchors
Extracting within-dataset neighbors

  |+++++++++++++++++++++++++++++++++++++++++++++     | 90% ~08m 35s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 6577 anchors
Filtering anchors
    Retained 2921 anchors
Extracting within-dataset neighbors

  |++++++++++++++++++++++++++++++++++++++++++++++    | 91% ~07m 27s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 6568 anchors
Filtering anchors
    Retained 2789 anchors
Extracting within-dataset neighbors

  |+++++++++++++++++++++++++++++++++++++++++++++++   | 92% ~06m 20s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 1650 anchors
Filtering anchors
    Retained 896 anchors
Extracting within-dataset neighbors

  |+++++++++++++++++++++++++++++++++++++++++++++++   | 94% ~05m 13s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 8661 anchors
Filtering anchors
    Retained 3880 anchors
Extracting within-dataset neighbors

  |++++++++++++++++++++++++++++++++++++++++++++++++  | 95% ~04m 12s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 9081 anchors
Filtering anchors
    Retained 4719 anchors
Extracting within-dataset neighbors

  |+++++++++++++++++++++++++++++++++++++++++++++++++ | 96% ~03m 12s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 4142 anchors
Filtering anchors
    Retained 2302 anchors
Extracting within-dataset neighbors

  |+++++++++++++++++++++++++++++++++++++++++++++++++ | 97% ~02m 06s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 4895 anchors
Filtering anchors
    Retained 2969 anchors
Extracting within-dataset neighbors

  |++++++++++++++++++++++++++++++++++++++++++++++++++| 99% ~01m 03s      

Running CCA
Merging objects
Finding neighborhoods
Finding anchors
    Found 5901 anchors
Filtering anchors
    Retained 3153 anchors
Extracting within-dataset neighbors

  |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=01h 20m 31s

obj <- IntegrateData(anchorset = anchors, dims = 1:30)

Merging dataset 7 into 4
Extracting anchors for merged samples
Finding integration vectors
Finding integration vector weights
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Integrating data
Merging dataset 11 into 9
Extracting anchors for merged samples
Finding integration vectors
Finding integration vector weights
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Integrating data
Merging dataset 10 into 9 11
Extracting anchors for merged samples
Finding integration vectors
Finding integration vector weights
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Integrating data
Merging dataset 12 into 8
Extracting anchors for merged samples
Finding integration vectors
Finding integration vector weights
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Integrating data
Merging dataset 6 into 5
Extracting anchors for merged samples
Finding integration vectors
Finding integration vector weights
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Integrating data
Merging dataset 13 into 9 11 10
Extracting anchors for merged samples
Finding integration vectors
Finding integration vector weights
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Integrating data
Merging dataset 3 into 1
Extracting anchors for merged samples
Finding integration vectors
Finding integration vector weights
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Integrating data
Merging dataset 4 7 into 5 6
Extracting anchors for merged samples
Finding integration vectors
Finding integration vector weights
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Integrating data
Merging dataset 5 6 4 7 into 1 3
Extracting anchors for merged samples
Finding integration vectors
Finding integration vector weights
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Integrating data
Merging dataset 8 12 into 9 11 10 13
Extracting anchors for merged samples
Finding integration vectors
Finding integration vector weights
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Integrating data
Merging dataset 2 into 1 3 5 6 4 7
Extracting anchors for merged samples
Finding integration vectors
Finding integration vector weights
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Integrating data
Merging dataset 1 3 5 6 4 7 2 into 9 11 10 13 8 12
Extracting anchors for merged samples
Finding integration vectors
Finding integration vector weights
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Integrating data
Adding a command log without an assay associated with it

proc.time() - ptm

    user   system  elapsed 
5130.765  320.437 5458.036 

obj <- ScaleData(obj, verbose = FALSE)
obj <- RunPCA(obj, npcs = 30, verbose = FALSE)

obj <- RunUMAP(obj, dims = 1:30, verbose=FALSE, reduction.name = "umap")

DimPlot(obj, reduction = "umap", group.by = "sample_new", label.size = 5,  pt.size = 0) +
  theme(axis.text.x=element_blank(),
        axis.ticks.x=element_blank(),
        axis.text.y=element_blank(),
        axis.ticks.y=element_blank(),
        text=element_text(size=18))
ggsave("covid_seurat_sample.pdf")

Saving 7.29 x 4.5 in image

DimPlot(obj, reduction = "umap", group.by = "sample_new", label.size = 10,  pt.size = 0) +
  theme(axis.text.x=element_blank(),
        axis.ticks.x=element_blank(),
        axis.text.y=element_blank(),
        axis.ticks.y=element_blank(),
        text=element_text(size=30))
ggsave("covid_seurat_sample.png", height=12, width=18, dpi = 100)

DimPlot(obj, reduction = "umap", group.by = "celltype", label = T, repel=T, label.size = 5,  pt.size = 0) +
  theme(axis.text.x=element_blank(),
        axis.ticks.x=element_blank(),
        axis.text.y=element_blank(),
        axis.ticks.y=element_blank(),
        text=element_text(size=18))
ggsave("covid_seurat_label.pdf")

Saving 7.29 x 4.5 in image

DimPlot(obj, reduction = "umap", group.by = "celltype", label = T, repel=T, label.size = 10,  pt.size = 0) +
  theme(axis.text.x=element_blank(),
        axis.ticks.x=element_blank(),
        axis.text.y=element_blank(),
        axis.ticks.y=element_blank(),
        text=element_text(size=30))
ggsave("covid_seurat_label.png", height=12, width=18, dpi = 100)

saveRDS(obj, "covid-seurat.RDS")